# Name

sxresolution - FSCM resolution measures: Compute overall and local resolution measures using a pair of half-maps.

# Usage

*Usage in command lines*:

sxresolution.py firstvolume secondvolume maskfile outputdir --wn=window_size --step=shell_step_size --cutoff=res_cutoff --res_overall=overall_resolution --radius=radius --fsc=output_file_name --MPI

### Typical usage

** sxresolution.py refinementdir/main002/vol0.hdf refinementdir/main002/vol2.hdf outputdir --radius=28 **

## Input

- firstvolume
- First half-volume: (default required string)
- secondvolume
- Second half-volume: (default required string)
- maskfile
- 3D mask: Defines the region within which FSCM will be computed. (default none)
- outputdir
- Output directory: results will be written to this directory. If it does not exist it will be created.
- wn
- FSCM box size: Defines the size of a 3D box within which local FSCM values will be computed. (default 15)
- step
- Fourier shell step size [Pixels]: (default 1.0)
- lfi
- LFI: Low Fourier index to begin calculations from (default 1)
- hfi
- HFI: High Fourier index to end calculations on (default nx//2-2)
- significance
- SIGNIFICANCE: Significance level for the Upper Confidence Interval. (default 0.99, which corresponds to 1%)
- sigmag
- SIGMAG: sigma of the Fourier space Gaussian window in pixels (default 1.0)
- ndf_reduce
- NDF_REDUCE: Reduction of ndf due to point group symmetry, for example for D3 set to 6 (default 1.0)
- cutoff
- Resolution cut-off [1/Pixel]: Cut-off for the Local FSCM CI. (default 0.143)
- radius
- Mask radius [Pixels]: If there is no maskfile, sphere with r=radius will be used. (default -1)
- local_fsc
- LOCAL_FSC: Set to 1 to compute local resolution volume (default 0).
- nthreads
- NTHREADS: Number of threads (mainly for 3D FFT) (default 4)

## Output

- outputdir
- results will be written to this directory
Output volume: Each voxel contains the resolution for this area in absolute frequency units. (default required string)

# Description

- Local resolution values are computed within small windowed areas (size wn^3). Due to small sample size the values are inaccurate and tend to underestimate resolution. Therefore, option res_overall allows to calibrate the average value of all local resolutions to the overall resolution, as estimated by the FSC between two full size volumes. I This value has to be independently obtained by the user - for example using sximgstat.py to compute (masked) FSC from half-volumes and reading the absolute frequency crresponding to 0.5 (or other) cut-off value.

# Method

# Reference

# Author / Maintainer

Pawel Penczek

# Keywords

- category 1
- APPLICATIONS

# Files

sxresolution.py

# See also

# Maturity

- stable
- works for most people, has been tested; test cases/examples available.

# Bugs

None. It is perfect.